Package com.compomics.util.experiment.identification.protein_sequences.digestion

Class IteratorFactory

java.lang.Object

com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory

public class IteratorFactory
extends Object

The iterator goes through a sequence and lists possible peptides with their fixed modifications.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor	Description
IteratorFactory()	Empty default constructor
IteratorFactory(ArrayList<String> fixedModifications)	Constructor with 2 Xs allowed.
IteratorFactory(ArrayList<String> fixedModifications, Integer maxX)	Constructor.

Method Summary

Modifier and Type	Method	Description
SequenceIterator	getSequenceIterator(String sequence, DigestionParameters digestionPreferences, double massMin, double massMax)	Returns a sequence iterator for the given protein sequence and digestion preferences.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

IteratorFactory

public IteratorFactory()

Empty default constructor

IteratorFactory

public IteratorFactory(ArrayList<String> fixedModifications,
 Integer maxX)

Constructor.

Parameters:

fixedModifications - a list of fixed modifications to consider when iterating the protein sequences.

maxX - The maximal number of Xs allowed in a sequence to derive the possible peptides

IteratorFactory

public IteratorFactory(ArrayList<String> fixedModifications)

Constructor with 2 Xs allowed.

Parameters:

fixedModifications - a list of fixed modifications to consider when iterating the protein sequences.

Method Details

getSequenceIterator

public SequenceIterator getSequenceIterator(String sequence,
 DigestionParameters digestionPreferences,
 double massMin,
 double massMax)
                                     throws InterruptedException

Returns a sequence iterator for the given protein sequence and digestion preferences.

Parameters:

sequence - the sequence to iterate

digestionPreferences - the digestion preferences to use

massMin - the minimal mass of a peptide

massMax - the maximal mass of a peptide

Returns:

a sequence iterator

Throws:

InterruptedException - exception thrown if a thread is interrupted